Job ID = 2001139 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:22:50 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T18:22:53 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T18:22:53 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T18:24:23 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T18:24:23 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T18:25:51 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 30,028,210 reads read : 30,028,210 reads written : 30,028,210 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:46 30028210 reads; of these: 30028210 (100.00%) were unpaired; of these: 1174423 (3.91%) aligned 0 times 19951751 (66.44%) aligned exactly 1 time 8902036 (29.65%) aligned >1 times 96.09% overall alignment rate Time searching: 00:11:47 Overall time: 00:11:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5593022 / 28853787 = 0.1938 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 04:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:01:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:01:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:01:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:33: 1000000 INFO @ Fri, 05 Jul 2019 04:01:34: 1000000 INFO @ Fri, 05 Jul 2019 04:01:37: 1000000 INFO @ Fri, 05 Jul 2019 04:01:42: 2000000 INFO @ Fri, 05 Jul 2019 04:01:44: 2000000 INFO @ Fri, 05 Jul 2019 04:01:46: 2000000 INFO @ Fri, 05 Jul 2019 04:01:51: 3000000 INFO @ Fri, 05 Jul 2019 04:01:52: 3000000 INFO @ Fri, 05 Jul 2019 04:01:56: 3000000 INFO @ Fri, 05 Jul 2019 04:02:00: 4000000 INFO @ Fri, 05 Jul 2019 04:02:00: 4000000 INFO @ Fri, 05 Jul 2019 04:02:06: 4000000 INFO @ Fri, 05 Jul 2019 04:02:08: 5000000 INFO @ Fri, 05 Jul 2019 04:02:08: 5000000 INFO @ Fri, 05 Jul 2019 04:02:16: 5000000 INFO @ Fri, 05 Jul 2019 04:02:16: 6000000 INFO @ Fri, 05 Jul 2019 04:02:17: 6000000 INFO @ Fri, 05 Jul 2019 04:02:24: 7000000 INFO @ Fri, 05 Jul 2019 04:02:25: 7000000 INFO @ Fri, 05 Jul 2019 04:02:26: 6000000 INFO @ Fri, 05 Jul 2019 04:02:32: 8000000 INFO @ Fri, 05 Jul 2019 04:02:33: 8000000 INFO @ Fri, 05 Jul 2019 04:02:35: 7000000 INFO @ Fri, 05 Jul 2019 04:02:40: 9000000 INFO @ Fri, 05 Jul 2019 04:02:42: 9000000 INFO @ Fri, 05 Jul 2019 04:02:45: 8000000 INFO @ Fri, 05 Jul 2019 04:02:48: 10000000 INFO @ Fri, 05 Jul 2019 04:02:50: 10000000 INFO @ Fri, 05 Jul 2019 04:02:55: 9000000 INFO @ Fri, 05 Jul 2019 04:02:57: 11000000 INFO @ Fri, 05 Jul 2019 04:02:58: 11000000 INFO @ Fri, 05 Jul 2019 04:03:04: 10000000 INFO @ Fri, 05 Jul 2019 04:03:05: 12000000 INFO @ Fri, 05 Jul 2019 04:03:06: 12000000 INFO @ Fri, 05 Jul 2019 04:03:13: 13000000 INFO @ Fri, 05 Jul 2019 04:03:14: 11000000 INFO @ Fri, 05 Jul 2019 04:03:14: 13000000 INFO @ Fri, 05 Jul 2019 04:03:21: 14000000 INFO @ Fri, 05 Jul 2019 04:03:22: 14000000 INFO @ Fri, 05 Jul 2019 04:03:23: 12000000 INFO @ Fri, 05 Jul 2019 04:03:29: 15000000 INFO @ Fri, 05 Jul 2019 04:03:30: 15000000 INFO @ Fri, 05 Jul 2019 04:03:33: 13000000 INFO @ Fri, 05 Jul 2019 04:03:37: 16000000 INFO @ Fri, 05 Jul 2019 04:03:39: 16000000 INFO @ Fri, 05 Jul 2019 04:03:43: 14000000 INFO @ Fri, 05 Jul 2019 04:03:45: 17000000 INFO @ Fri, 05 Jul 2019 04:03:46: 17000000 INFO @ Fri, 05 Jul 2019 04:03:52: 15000000 INFO @ Fri, 05 Jul 2019 04:03:53: 18000000 INFO @ Fri, 05 Jul 2019 04:03:54: 18000000 INFO @ Fri, 05 Jul 2019 04:04:02: 19000000 INFO @ Fri, 05 Jul 2019 04:04:02: 16000000 INFO @ Fri, 05 Jul 2019 04:04:02: 19000000 INFO @ Fri, 05 Jul 2019 04:04:11: 20000000 INFO @ Fri, 05 Jul 2019 04:04:11: 20000000 INFO @ Fri, 05 Jul 2019 04:04:12: 17000000 INFO @ Fri, 05 Jul 2019 04:04:19: 21000000 INFO @ Fri, 05 Jul 2019 04:04:20: 21000000 INFO @ Fri, 05 Jul 2019 04:04:21: 18000000 INFO @ Fri, 05 Jul 2019 04:04:28: 22000000 INFO @ Fri, 05 Jul 2019 04:04:29: 22000000 INFO @ Fri, 05 Jul 2019 04:04:31: 19000000 INFO @ Fri, 05 Jul 2019 04:04:38: 23000000 INFO @ Fri, 05 Jul 2019 04:04:38: 23000000 INFO @ Fri, 05 Jul 2019 04:04:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:04:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:04:40: #1 total tags in treatment: 23260765 INFO @ Fri, 05 Jul 2019 04:04:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:04:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:04:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:04:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:04:40: #1 total tags in treatment: 23260765 INFO @ Fri, 05 Jul 2019 04:04:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:04:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:04:41: 20000000 INFO @ Fri, 05 Jul 2019 04:04:41: #1 tags after filtering in treatment: 23260665 INFO @ Fri, 05 Jul 2019 04:04:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:04:41: #1 finished! INFO @ Fri, 05 Jul 2019 04:04:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:04:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:04:41: #1 tags after filtering in treatment: 23260665 INFO @ Fri, 05 Jul 2019 04:04:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:04:41: #1 finished! INFO @ Fri, 05 Jul 2019 04:04:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:04:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:04:44: #2 number of paired peaks: 6977 INFO @ Fri, 05 Jul 2019 04:04:44: start model_add_line... INFO @ Fri, 05 Jul 2019 04:04:44: #2 number of paired peaks: 6977 INFO @ Fri, 05 Jul 2019 04:04:44: start model_add_line... INFO @ Fri, 05 Jul 2019 04:04:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:04:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:04:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:04:44: #2 predicted fragment length is 38 bps INFO @ Fri, 05 Jul 2019 04:04:44: #2 alternative fragment length(s) may be 38,581 bps INFO @ Fri, 05 Jul 2019 04:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.05_model.r WARNING @ Fri, 05 Jul 2019 04:04:44: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 04:04:44: #2 You may need to consider one of the other alternative d(s): 38,581 WARNING @ Fri, 05 Jul 2019 04:04:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 04:04:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:04:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:04:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:04:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:04:44: #2 predicted fragment length is 38 bps INFO @ Fri, 05 Jul 2019 04:04:44: #2 alternative fragment length(s) may be 38,581 bps INFO @ Fri, 05 Jul 2019 04:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.10_model.r WARNING @ Fri, 05 Jul 2019 04:04:44: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 04:04:44: #2 You may need to consider one of the other alternative d(s): 38,581 WARNING @ Fri, 05 Jul 2019 04:04:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 04:04:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:04:50: 21000000 INFO @ Fri, 05 Jul 2019 04:05:00: 22000000 INFO @ Fri, 05 Jul 2019 04:05:09: 23000000 INFO @ Fri, 05 Jul 2019 04:05:11: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:05:11: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:05:11: #1 total tags in treatment: 23260765 INFO @ Fri, 05 Jul 2019 04:05:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:05:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:05:12: #1 tags after filtering in treatment: 23260665 INFO @ Fri, 05 Jul 2019 04:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:05:12: #1 finished! INFO @ Fri, 05 Jul 2019 04:05:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:05:15: #2 number of paired peaks: 6977 INFO @ Fri, 05 Jul 2019 04:05:15: start model_add_line... INFO @ Fri, 05 Jul 2019 04:05:15: start X-correlation... INFO @ Fri, 05 Jul 2019 04:05:15: end of X-cor INFO @ Fri, 05 Jul 2019 04:05:15: #2 finished! INFO @ Fri, 05 Jul 2019 04:05:15: #2 predicted fragment length is 38 bps INFO @ Fri, 05 Jul 2019 04:05:15: #2 alternative fragment length(s) may be 38,581 bps INFO @ Fri, 05 Jul 2019 04:05:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.20_model.r WARNING @ Fri, 05 Jul 2019 04:05:15: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 04:05:15: #2 You may need to consider one of the other alternative d(s): 38,581 WARNING @ Fri, 05 Jul 2019 04:05:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 04:05:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:05:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:05:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:06:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.05_summits.bed INFO @ Fri, 05 Jul 2019 04:06:35: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (2563 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.10_summits.bed INFO @ Fri, 05 Jul 2019 04:06:35: Done! pass1 - making usageList (49 chroms): 5 millis pass2 - checking and writing primary data (1608 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX016351/ERX016351.20_summits.bed INFO @ Fri, 05 Jul 2019 04:07:06: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (886 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。